A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Tsai, Chia-Feng; Wang, Yi-Ting; Hsu, Chuan-Chih; Kitata, Reta Birhanu; Chu, Rosalie K.; Velickovic, Marija; Zhao, Rui; Williams, Sarah M.; Chrisler, William B.; Jorgensen, Marda L.; Moore, Ronald J.; Zhu, Ying; Rodland, Karin D.; Smith, Richard D.; Wasserfall, Clive H.; Shi, Tujin; Liu, Tao

doi:10.1038/s42003-022-04400-x

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Journal Article · Tue Jan 17 23:00:00 EST 2023 · Communications Biology

DOI:https://doi.org/10.1038/s42003-022-04400-x· OSTI ID:1922420

^[1]; ^[1]; Hsu, Chuan-Chih ^[2]; ^[1]; ^[1]; Velickovic, Marija ^[3]; Zhao, Rui ^[1]; Williams, Sarah M. ^[3]; Chrisler, William B. ^[1]; Jorgensen, Marda L. ^[4]; ^[1]; ^[3]; ^[1]; ^[1]; ^[4]; ^[1]; ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Academia Sinica, Taipei (Taiwan)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Univ. of Florida, Gainesville, FL (United States). Diabetes Institute

Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); Brain Initiative Cell Census Network (BICCN); National Institute of General Medical Sciences (NIGMS); NCI Innovative Molecular Analysis Technologies (IMAT)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1922420

Report Number(s):: PNNL-SA-171979

Journal Information:: Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 6; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Boosting to Amplify the Signal with Isobaric Labeling (BASIL)
Surfactant-assisted One-Pot (SOP) sample preparation
nanoscale phosphoproteome
near single-cell
tip IMAC

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

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